AMBER: Modelling dsDNA less than 10bp

From: Lena Dolghih <>
Date: Fri, 21 Jul 2006 09:15:16 -0400 (EDT)


I was trying to run GB dynamics with a short DNA (4 bp) and its structure gets
distorted within 1 ns. I noticed that in all major papers on GB simulations at
least 10bp nucleic acids are used. I was wondering if it's possible to model
shorter dsDNA at all (maybe in explicit solvent) or, if not, what is the reason
that the structure is not maintained? What is the case in reality - does such
short DNA exist as a stable structure in vivo?

Thank you for your help,

Lena Dolghih
Department of Chemistry
University of Florida

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jul 23 2006 - 06:07:12 PDT
Custom Search